A Roman Catholic priest in Woburn was indicted yesterday on charges he sexually molested an 11-year-old altar boy in a church rectory in September.

Prosecutors allege that Rev. Paul Manning, 53, touched the genitals of the boy while the two were in St. Charles rectory on the evening of Sunday, Sept. 5.

An adult whom Father Manning did not see in the rectory claimed to have witnessed the alleged incident and reported it to church officials, said Martha Coakley, chief prosecutor of the child abuse unit for the Middlesex district attorney.

Coakley said church officials first contacted the boy's family, whose son had not told them about the alleged incident, and then called the district attorney's office.

It is quite common for child victims of sexual assault to repress the incident and not confide in their parents, Coakley said, but added: "this case is a little different because there was a witness to the event."

A grand jury yesterday charged Father Manning with one count of indecent assault and battery of a minor. He will be arraigned early next month in Middlesex Superior Court.

Father Manning and his attorney, Eileen Donoghue, could not be reached last night for comment.

The accused priest, who has served at St. Charles Church since June 1992, has been on administrative leave during the investigation, said Jim Healey, co-chair of the church's parish council.

Healey said another priest has temporarily replaced Father Manning at St. Charles, one of the largest parishes in Woburn.

Before going there, Father Manning served elsewhere in Massachusetts, but prosecutors would not disclose the names of his previous parishes.

"We have absolutely no other reason to think there are any other victims," Coakley said.

Coakley said that in the 2 1/2 years she has headed the child abuse unit, she has received no other allegations of priests molesting children in Middlesex County.